From: JC Gumbart (
Date: Wed Mar 10 2010 - 23:26:30 CST

I guess what you need is the glycerol topology? I'm pretty sure this is in
Charmm - see MacKerell's website for the full forcefield topology and
parameter set:



From: Roshan Tasgaonkar []
Sent: Wednesday, March 10, 2010 11:19 PM
Subject: RE: vmd-l:


I am familiar with running basic MD simulations, the problem i'm having is
in inputting many glycerin molecules because they are very small and its not
possible to create a psf for them which can than be solvated




Subject: RE: vmd-l:
Date: Wed, 10 Mar 2010 23:00:43 -0600


Try the VMD and NAMD tutorials to start.



From: [] On Behalf Of
Roshan Tasgaonkar
Sent: Wednesday, March 10, 2010 10:56 PM
Subject: vmd-l:


Hey guys!


I want to run a simulation on linux where i have a insulin solvated in a box
of water with a lot of glycerins in the box. I am not sure how to start
doing this, i know how to solvate and know the basics of linux. I heard it
has something to do with .inp files? could someone outline a way for me to
be able to run this MD simulation




Roshan Tasgaonkar



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